crossing96/oncoscreening huggingface dataset:
Survival in Responders and Nonresponders of Neoadjuvant and Induction Chemotherapy in Invasive Urothelial Carcinoma of the Urinary Bladder: A Clinical and Pathological Stage-Matched Analysis.	INTRODUCTION/BACKGROUND: A recent study reported that patients with residual urothelial carcinoma of the bladder subsequent to neoadjuvant/induction chemotherapy (NAIC) prior to RC exhibited inferior oncological outcomes in comparison to pathological stage-matched patients who underwent upfront RC. Our hypothesis is that this may be ascribed to variations in preoperative CT-stage rather than the impact of chemotherapy. PATIENTS AND METHODS: This retrospective multicentre study included 513 patients who underwent RC for cT2-4N0-3M0 disease between 2010 and 2017. Patients were categorized based on pathological outcomes: pathological complete response (pCR, (y)pT0N0), complete downstaging (pCD, (y)pT0/is/a/1N0) and residual muscle-invasive and/or node positive disease (rMIBC, (y)pT2-4N0 and/or (y)pN1-3). RESULTS: Of the total cohort, 175 (34.1%) patients underwent NAIC+RC, while 338 (65.9%) underwent upfront RC. NAIC+RC patients exhibited lower age and CCI-scores, along with higher cT&N-stage (all P-values < .001). The mOS was 60.5 months for NAIC+RC and 49.4 months for upfront RC (P-value = .171). In patients with rMIBC, survival was inferior after NAIC+RC compared to upfront RC. However, the clinical stage distribution between NAIC+RC and upfront RC was imbalanced, with 3% versus 49% cT2N0 patients and 47% versus 9% cT4b and/or N+ patients, respectively. Following adjustments for cT & N-stage, age, and CCI-scores in multivariable Cox proportional-hazards analysis, worse OS was associated with upfront RC (HR 1.52, [95% CI, 1.11-2.10], P-value = .009). CONCLUSION: The observed inferior survival in cT2-4N0-3M0 patients with rMIBC after NAIC+RC compared to those undergoing upfront RC resulted from worse preoperative characteristics, including clinical stage. The representation of clinical disease stage should not be overlooked in survival analyses.	bladder
The N6-methyladenosine reader IGF2BP3 promotes bladder cancer progression through enhancing HSP90AB1 expression.	N(6)-methyladenosine (m(6)A) is the most abundant RNA modification in mammalian cells, and has emerged as an important player in tumour development through post-transcriptional gene regulation. In this study, we found that the m(6)A reader protein IGF2BP3 was the most upregulated m(6)A modifier in bladder cancer through the proteomic analysis of 17 pairs of human bladder cancer tissues and adjacent normal bladder tissues, for which the expression was also positively correlated with higher tumour stage and poorer prognosis. In vitro and in vivo assays demonstrated the powerful oncogenic function of IGF2BP3 in bladder cancer. Further combined analyses of RNA-sequencing, m(6)A-sequencing, and RIP (RNA Binding Protein Immunoprecipitation)-sequencing, as well as site-directed mutagenesis assays and RIP-qPCR identified m(6)A-tagged HSP90AB1 mRNA as a direct target of IGF2BP3. Mechanistically, through in vitro and in vivo assays, as well as clinical sample analysis, we demonstrated that IGF2BP3 modulated the expression of HSP90AB1 in an m(6)A modification-dependent manner, thus activating the PI3K/AKT-signaling pathway, and promoting the development of bladder cancer. Collectively, our study highlights the critical role of the IGF2BP3-HSP90AB1-signaling axis in bladder cancer progression, which may serve as a promising therapeutic approach for bladder cancer.	bladder
Assessing the clinical efficacy of neoadjuvant intravesical Mitomycin C in naïve non-muscle invasive urinary bladder cancer: A systematic review and meta-analysis.	BACKGROUND AND OBJECTIVE: Naïve non-muscle invasive bladder cancer (NMIBC) is commonly treated with transurethral resection (TURBT), but recurrence and progression remain concerns. This meta-analysis, the first we have conducted on this topic, compared recurrence and progression rates between patients treated with neoadjuvant Mitomycin C (MMC) and the control group (TURBT alone). METHODS: Relevant articles were identified and appraised through a structured literature assessment. Databases searched included PubMed, Medline, Scopus, and Science Direct. Duplicate publications, book sections, conference papers, encyclopedias, case reports, magazine articles, presentations, theses, protocols, systematic reviews, and meta-analyses were excluded. Heterogeneity was assessed using the I(2). KEY FINDINGS AND LIMITATIONS: The meta-analysis evaluated recurrence rates, progression rates, and adverse events. No heterogeneity was observed (I(2)=0 %). The pooled odd ratio (OR) for recurrence was 2.554 (95 % CI: 1.637-3.986), indicating a significant decrease in recurrence for the MMC group (P < 0.001). For progression rates, the overall pooled OR was 1.508 (95 % CI: 0.832-2.734), suggesting that the MMC group showed a lower progression rate. However, this difference was not statistically significant (P = 0.176).Adverse events varied, with the MMC group showing fewer cases of hematuria (8.4 % vs. 34 %) but more irritative bladder symptoms. CONCLUSIONS AND CLINICAL IMPLICATIONS: The meta-analysis suggests lower recurrence and progression rates in the neoadjuvant MMC group compared to the control group. Both groups experienced a comparable range of adverse events, suggesting that both treatment approaches exhibit a similar safety profile. Larger and more randomized controlled trials (RCT) are needed to confirm MMC's effectiveness in NIMBC treatment and establish its role in clinical practice.	bladder
Comprehensive analysis of RNA methylation-related genes to identify molecular cluster for predicting prognosis and immune profiles in bladder cancer.	m6A, m5C and m7G are common types of RNA methylation modifications that are widely involved in key mechanisms regulating malignancy. However, the role of RNA methylation-related genes in the immune microenvironment of bladder cancer (BLCA) remains elusive. In this study, we established RNA methylation molecular subtypes by analyzing the TCGA and GEO datasets. Risk model and nomogram were constructed by LASSO and multivariate Cox regression analysis and validated by external datasets. Genetic variations, functional enrichment analysis and immune cell infiltration were analyzed. The expression levels of hub genes were detected by real-time polymerase chain reaction (qRT-PCR) and immunohistochemistry (IHC). The effect of FN1 on cellular function was determined using experimental assays. Finally, we identified a 7-gene signature associated with BLCA prognosis. GSE19423 validated the predictive value of the risk model. The IMvigor210 data showed the model had promising predictive efficacy for BLCA immunotherapy. Significant differences in biological function, immune cell infiltration and drug sensitivity were observed between high- and low-risk groups. Furthermore, FN1 was upregulated in BLCA, as determined by qRT-PCR and IHC. Depletion of FN1 using siRNA impaired cell motility in T24 and 5637 cells. In conclusion, RNA methylation-related risk model can predict the prognosis, immune landscape and response to immunotherapy in BLCA. Among the 7-gene signature, FN1 is a pivotal gene that promotes the migration of bladder cancer cells.	bladder
Factor VIII, a coagulation cofactor, is a relevant survival factor in bladder cancer cell lines.	BACKGROUND: Factor (F)VIII, an essential coagulation cofactor and independent cancer-associated thrombotic risk factor, has recently been shown to be synthesized directly by a broad profile of cancers. With evident extracoagulative functions, it remains to be understood if FVIII can play a functional role in cancer. OBJECTIVES: Establish if FVIII plays a direct role in bladder cancer cell models. METHODS: Bladder cancer cell lines 5637 and ECV-304 were treated with recombinant human FVIII (rFVIII) B-domain-deleted or full-length rFVIII (rFVIII-FL) in low serum conditions, where cell cycle, migration, and cell survival were assessed. Cell cycle was measured by 7-aminoactinomycin D incorporation and migration by Transwell or wound healing assays. Cell survival was assessed by crystal violet (optical density 592) and 3-(4,5-dimethylthiazol-2-Yl)-2,5-diphenyltetrazolium bromide (optical density 570) assays. Cell adhesion was determined with integrin β(1) and α(V) protein levels, annexin-V-FITC/7-aminoactinomycin D staining, and Bcl2 with procaspase3 levels for apoptosis. Cancer cell-derived effects were assessed by silencing FVIII using short hairpin RNA. RESULTS: In both bladder cancer cell lines, cell cycle progression was pushed, and migration was advanced by rFVIII. More dramatic were the survival effects for rFVIII-FL, confirmed in a cell line of diverse origin, the osteosarcoma U2OS, through the maintenance of cell adhesion and inhibition of apoptosis. Further, silencing cell-derived FVIII retarded both cell cycle progression and migration. More importantly, cell survival was dramatically reduced and could be blocked by the administration of rFVIII-FL. CONCLUSION: Overall, this investigation highlights FVIII as a relevant survival factor in bladder cancer cells and provides evidence of its role in cancer.	bladder
Inhibition of Cyclin D1 by Novel Biguanide Derivative YB-004 Increases the Sensitivity of Bladder Cancer to Olaparib via Causing G0 / G1 Arrest.	Bladder cancer (BC) is the 10(th) most common type of tumor worldwide, and recently approved immunotherapies and FGFR inhibitors have been shown to improve the prognosis of only a very limited subset of BC patients. Thus, the quest for more effective drugs remains an urgent priority for improving the quality of life of more BC patients. Previously, we demonstrated that a novel biguanide YB-004 has potent antitumor activity. In this study, we found that the novel biguanide YB-004 interrupts the cell cycle by reducing the expression of cyclin D1, causing G0/G1 phase arrest, and suppresses homologous recombination (HR) by inhibiting Rad51, thereby increasing DNA damage and blocking BC cell proliferation. Interestingly, our results further revealed that cell accumulation in the S and G2/M phases is the main reason why HR-proficient BC cells are not sensitive to olaparib, as these phases are conducive to HR activation and DNA repair. Thus, YB-004 increased the sensitivity of BC cells to olaparib by reversing the cell cycle changes and HR activation caused by olaparib. Taken together, these findings suggest that the combination of YB-004 with olaparib has great potential for the clinical treatment of HR-proficient BC.	bladder
Quadratus lumborum block is feasible alternative to epidural block for postoperative analgesia after open radical cystectomy: surgical and oncological outcomes of a randomised clinical trial.	OBJECTIVE: The current lack of standardised perioperative pain management protocols for open radical cystectomy (ORC) underscores the need for alternative approaches to the longstanding tradition of epidural block. The aim of this study was to assess the impact of bilateral single injection quadratum lumborum block (QLB) on patients' recovery and complication rates compared with epidural analgesia after ORC in a single-centre, randomised, parallel-group trial including adult patients with bladder cancer. MATERIAL AND METHODS: Consecutive ORC patients were randomly allocated into QLB and the epidural group. The primary endpoint of this study was related to opioid consumption, and the results have been published earlier. This report focuses on secondary outcomes. RESULTS: This study included a total of 41 patients, with 20 patients in the QLB group and 21 patients in the epidural group. Finally, 39 patients were included in the analysis.  There was a trend for more frequent need for postoperative norepinephrine and fluid support in the epidural group but without statistical significance. Postoperative complication rate was similar. Two patients in the epidural group compared to none in the QLB group were rehospitalised within 30 and 90 days. Mortality rate within 90 days was higher in the epidural group (4 vs. 0 patients, P = 0.064). CONCLUSIONS: In this trial, there were no significant differences in surgical and oncological outcomes after ORC when QLB is compared with epidural block for postoperative analgesia.  Trial registration: ClinicalTrials.gov Identifier: NCT03328988.	bladder
Protocol for single-cell RNA sequencing and spatial transcriptomics of bladder Ewing sarcoma.	Single-cell RNA sequencing provides a deep understanding of gene expression patterns at the single-cell level, enabling researchers to study cellular heterogeneity and differentiation. Spatial transcriptomics, meanwhile, delivers spatial visualization and quantitative analysis of tissue sections. Here, we introduce a protocol to isolate single cells and obtain high-quality spatial transcriptomics data from bladder Ewing sarcoma tissue. We outline steps for sample collection, single-cell RNA sequencing, and spatial transcriptomics sequencing. For complete details on the use and execution of this protocol, please refer to Mao et al.(1).	bladder
Intracorporeal versus extracorporeal neobladder in robot-assisted radical cystectomy: perioperative, oncological, and functional outcomes from a single-institutional experience.	PURPOSE: To compare the perioperative, functional, and oncological outcomes of the intracorporeal neobladder (ICNB) and extracorporeal neobladder (ECNB) technique following robot-assisted radical cystectomy (RARC). METHODS: We reviewed our single-institutional, prospectively collected database for consecutive patients who underwent RARC with an ileum neobladder from July 2016 to February 2023. Patients were divided into 2 groups according to the approach of reconstruction (ICNB or ECNB). The chi-squared test and Wilcoxon test were used to summarize categorical and continuous variables, respectively. survival and complication outcomes were analyzed using Kaplan-Meier curves, multivariate logistic regression and Cox hazards models. RESULT: Among 304 patients, 190 ICNB patients and 114 ECNB patients were identified. A shorter median operative time (320 vs. 354 min; p = 0.001) and less median EBL (300 vs. 500 ml; p < 0.001) were recorded in the ICNB group. A significant difference in 90-d overall complications was detected between the 2 groups (49.5% vs. 61.4%; p = 0.043). Multivariate logistic regression analysis demonstrated that age, relapsed tumor and surgical approach (ECNB/ICNB) were individual predictive factors for 90-d overall complications. The functional outcomes and survival rates were comparable between the ICNB and ECNB groups. A Cox proportional hazards model indicated that higher pathological stage and pN status are predictors of both recurrence-free survival (RFS) and overall survival (OS). CONCLUSION: Compared with ECNB, ICNB significantly improves perioperative outcomes without compromising functional or oncological outcomes.	bladder
A CT-based interpretable deep learning signature for predicting PD-L1 expression in bladder cancer: a two-center study.	BACKGROUND: To construct and assess a deep learning (DL) signature that employs computed tomography imaging to predict the expression status of programmed cell death ligand 1 in patients with bladder cancer (BCa). METHODS: This retrospective study included 190 patients from two hospitals who underwent surgical removal of BCa (training set/external validation set, 127/63). We used convolutional neural network and radiomics machine learning technology to generate prediction models. We then compared the performance of the DL signature with the radiomics machine learning signature and selected the optimal signature to build a nomogram with the clinical model. Finally, the internal forecasting process of the DL signature was explained using Shapley additive explanation technology. RESULTS: On the external validation set, the DL signature had an area under the curve of 0.857 (95% confidence interval: 0.745-0.932), and demonstrated superior prediction performance in comparison with the other models. SHAP expression images revealed that the prediction of PD-L1 expression status is mainly influenced by the tumor edge region, particularly the area close to the bladder wall. CONCLUSIONS: The DL signature performed well in comparison with other models and proved to be a valuable, dependable, and interpretable tool for predicting programmed cell death ligand 1 expression status in patients with BCa.	bladder
Precision screening with sequential multi-algorithm reclassification technique (SMART): Saving bladders from unnecessary cystectomy.	Bladder cancer, when diagnosed at an advanced stage, often necessitates inevitable invasive intervention. Consequently, non-invasive biosensor-based cancer detection and AI-based precision screening are being actively employed. However, the misclassification of cancer patients as normal-referred to as false negatives-remains a significant concern, as it could lead to fatal outcomes in lifespan. Moreover, while ensemble techniques such as soft voting and other methods can improve model accuracy and reduce misclassification, their effectiveness is limited and not applicable to all diagnostic tasks. Here, we developed a double stage cancer screening system that utilizes a sensitive urinary electrical biosensor implemented with an AI model and XAI interpretation tools. This system is designed for screening bladder cancer, well-known for its notable recurrence and high tendency to advance from non-invasive muscle tumors to muscle-invasive tumors. Four urinary biomarkers (CK8, CK18, PD-1, PD-L1) were measured by a field-effect transistor biosensor, and along with gender and age information, patients underwent initial screening by the CatBoost classification model. Patients initially classified as normal were reclassified using local explanations from neural networks offering a different perspective than CatBoost. After the second-stage screening, all of the false negatives from the initial screening could be correctly reclassified as cancer patients. Furthermore, global explanation guides the improvement of the AI model to be trained on an appropriate set of biomarker features to achieve high accuracy.	bladder
Patient Preferences for Post-Radical Cystectomy Treatment in Muscle-Invasive Bladder Cancer: A Discrete Choice Experiment in Japan.	OBJECTIVES: This study aimed to assess the treatment preferences of Japanese patients with muscle-invasive bladder cancer (MIBC) by quantifying their trade-offs between treatment attributes using a discrete choice experiment (DCE). METHODS: A DCE was conducted among MIBC patients post-radical cystectomy. Participants were presented with hypothetical treatment options differing in attributes such as efficacy Disease-free survival (DFS), side effects, administration, and cost. Preference data were analyzed to determine each attribute's relative importance (RI), maximum acceptable risk (MAR), and willingness to trade efficacy (WTTE). RESULTS: Out of 105 patients surveyed, 101 were included in the final analysis. The DCE revealed that DFS had the highest RI (30.3%), followed by annual treatment cost (27.7%) and risk of severe side effects (26.8%). While MAR analysis indicated that patients were willing to accept some increase in side effects risk for significant gains in DFS, WTTE results showed a sensitivity to side effect severity and treatment costs, with patients often willing to trade off DFS for improvements in risks and costs. In subgroup analyses, such as pathological stage, age, and employment status, the trends for each subgroup were the same as those of the overall population. However, the magnitude of RI varied among patients with different characteristics. For example, younger patients preferred short-term treatment duration over longer, employed patients tended to favor long-term treatment duration. CONCLUSIONS: This study is the first to demonstrate the treatment preferences of Japanese MIBC patients who underwent radical cystectomy, and these results can inform treatment selection based on patient preferences. TRIAL REGISTRATION: Japan Registry of Clinical Trials: jRCT1030220680.	bladder
Separated Transfixing Uretero-Enteral Anastomosis Method in Robot-Assisted Radical Cystectomy with Ileal Conduit: Early Induction Experience.	INTRODUCTION: This study aimed to evaluate the initial outcomes of a novel transfixing uretero-enteral anastomosis technique in robot-assisted radical cystectomy (RARC) with ileal conduit in an intracorporeal urinary diversion (ICUD), focusing on its potential to reducing the incidence of uretero-enteric anastomotic stricture. METHODS: The study subjects were 11 patients who underwent RARC and ileal conduit created as an ICUD at a single cancer center between 2022 and 2024. The technique involved opening the ventral side of the oral end of the separated ileum approximately 5 cm apart. Two small holes were made 2 cm from the oral end on the dorsal side, through which the ureter passed to the luminal side. The distal end of the ureter was spatulated, and four knotted sutures were placed at the base using 4-0 absorbable sutures. The distal end of the ureter was anchored using two knotted sutures, and the liberated portion was closed using 3-0 absorbable suture in a running fashion. RESULTS: The median total operation time was 418 min (range: 269-467 min), with a median console time of 93 min (range: 80-129 min) for urinary diversion. Two patients required temporary stent reinsertion because of hydronephrosis; however, no pyelonephritis occurred. Two patients (18.2%) had complications of Clavien-Dindo classification 3 or higher, both of which only required temporary stent reinsertion. Postoperative renal function was preserved in all the patients. CONCLUSIONS: In our initial experience, the transfixing uretero-enteral anastomosis technique was successful in stabilizing anastomoses in ICUD.	bladder
Comprehensive pan-cancer single-cell analysis reveals glycolysis-related signatures as predictive biomarkers for immunotherapy response and their role in bladder cancer.	Glycolysis is a vital metabolic biological process in tumor progression and immune modulation. This study comprehensively investigated the roles of glycolysis in pan-cancer, especially in bladder cancer. Exploration of 34 single-cell RNA sequencing (scRNA-seq) cohorts, eight ICI-treated bulk RNA-seq cohorts, and TCGA bulk pan-cancer RNA-seq cohorts uncovered a Glycolysis.Sig which strongly correlated with immunotherapy response and demonstrated excellent predictive performance in prognosis and immune response. Hub-Glycolysis.Sig exhibited varying interactions with the immune microenvironment based on cancer type. In bladder cancer, higher glycolysis risk scores correlated with poorer prognosis, with distinct immune infiltration characteristics between subtypes. scRNA-seq revealed high glycolysis levels in bladder epithelial cells. COPB2 was highly expressed in bladder cancer, promoting cell proliferation, migration, and glycolytic activity in vitro and in vivo. Our large-scale data analysis confirmed the negative correlation between glycolysis and immunotherapy outcomes, identifying Glycolysis.Sig as a novel predictive biomarker. Hub-Glycolysis.Sig provides clinical insights for bladder cancer therapy strategies, while COPB2 and other potential therapeutic targets facilitate personalized cancer treatment.	bladder